Bioinformatics 526 - Sitemaker

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Oct 1, 2013 (3 years and 6 months ago)

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Bioinformatics 551 (3 Credits
)

Proteome Informatics


Course
Master
:

Alexey I. Nesvizhskii

(
nesvi@umich.edu)


Graduate Student Instructor:

Andrew P. Hodges


Class Schedule:

Tuesdays and Thursdays 1:00 PM


2:30 PM

Location:

Room 2062 Palmer Commons (PC)


Prerequisites:
This is an inte
rdisciplinary course, so stu
dents are expected to come from
different
backgrounds. Ideal prior training includes u
pper leve
l or graduate level

Statistics

or other

courses
covering data analysis methods; Chemistry,
Biochemistr
y, Molecular Biology, or Cellular Biology; or
permission of instructor.


Topics to be covered

1. Introduction to proteomics


P
rotein chemistry, mass spectrometry, liquid chromatography

2.
Mass spectrometry

(MS)
-
based p
eptide and protein identification


Co
mputational methods:
database searching, spectrum

libraries, de novo sequencing


P
rotein inference

and related issues


Assessment of

statistical confidence in peptide and protein identifications

3.
Analysis of p
ost
-
translational modifications

(PTM)


P
ho
s
p
ho
rylation,

glyco
sylation
, etc.


C
omputational issues and algorithms specific to PTM analysis

4
.
Quantitative proteomics


Stable isotope labeling
-
based methods (iTRAQ, SILAC etc.)


Label
-
free methods (
spectrum counting)


Computational methods and s
tatisti
cal analysis




Application of quantitative proteomics

to the analysis of cell organelles and ma
cro
-
molecular

complexes

5. Protein interaction networks


MS
-
based reconstruction of protein interaction networks and protein complexes


Computational analysis
and modeling of protein interaction networks


6
. Data mining and analysis of large scale
proteomic
datasets


Proteomic d
atabases


Proteotypic peptides


Peptide fragmentation trends


Genome annotation using mass spectrometry

7
. Cli
nical applications


Cance
r Informatics


Biomarkers



Targeted analysis using multiple
-
reaction monitoring (MRM)

8
. Non
-
mass spectrometry
-
based proteomics methods


Phage displays,
p
rotein/peptide arrays, etc.

9
. Proteomics and systems b
iology


Integrative analysis


Connecting prote
omic and transcriptional data


Pathway analysis



Grading
:
E
ach exam worth
15
% (x 2 exams) =
3
0
%

Homework

= 25%

Quizzes =
10%

Group Project

= 2
5
% (more details will be given later this term)

Attendance

= 10%


Homework Assignments:

Homework assignments wil
l be assigned weekly, and will be due one week later at the start of class.
In most cases, you will receive assignments on Thursdays and must complete the assignments prior
to the next Thursday’s class.


Group Project:

You wi
ll work in groups of students
(3
-
5 individuals/group) and develop a new
proteome
bioinformatics pipeline or methodology, or perform analysis of a proteomic dataset

using existing
computational tools.

More details will be provided later in the term.


Examinations:

Exams will be take
-
ho
me format. You may use any reference materials (books, journals, online
sources) for the examination. You will be given approximately one week to complete the exam.
More details will be given closer to examination time.